메뉴 건너뛰기




Volumn 77, Issue 1, 2009, Pages 159-173

Native secondary structure topology has near minimum contact energy among all possible geometrically constrained topologies

Author keywords

Contact energy; Electron microscopy; Protein structure prediction; Secondary structure; Topology

Indexed keywords

PROTEIN;

EID: 70349337592     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.22427     Document Type: Article
Times cited : (17)

References (54)
  • 1
    • 0032917069 scopus 로고    scopus 로고
    • Protein structural topology: Automated analysis and diagrammatic representation
    • Westhead DR, Slidel TW, Flores TP, Thornton JM. Protein structural topology: automated analysis and diagrammatic representation. Protein Sci 1999;8:897-904.
    • (1999) Protein Sci , vol.8 , pp. 897-904
    • Westhead, D.R.1    Slidel, T.W.2    Flores, T.P.3    Thornton, J.M.4
  • 2
    • 0027946925 scopus 로고
    • Automating the identification and analysis of protein beta-barrels
    • Flower DR. Automating the identification and analysis of protein beta-barrels. Protein Eng 1994;7:1305-1310.
    • (1994) Protein Eng , vol.7 , pp. 1305-1310
    • Flower, D.R.1
  • 3
    • 0028175519 scopus 로고
    • Beta-sheet topology. a new system of nomenclature
    • Flower DR. Beta-sheet topology. A new system of nomenclature. FEBS Lett 1994;344:247-250.
    • (1994) FEBS Lett , vol.344 , pp. 247-250
    • Flower, D.R.1
  • 4
    • 0029549858 scopus 로고
    • FOLD: Integrated analysis and display of protein secondary structure
    • Flower DR. FOLD: integrated analysis and display of protein secondary structure. J Mol Graph 1995;13:377-384.
    • (1995) J Mol Graph , vol.13 , pp. 377-384
    • Flower, D.R.1
  • 5
    • 0028578645 scopus 로고
    • Interhelical contacts determining the architecture of alpha-helical globular proteins
    • Grigoriev IV, Mironov AA, Rakhmaninova AB. Interhelical contacts determining the architecture of alpha-helical globular proteins. J Biomol Struct Dyn 1994;12:559-572.
    • (1994) J Biomol Struct Dyn , vol.12 , pp. 559-572
    • Grigoriev, I.V.1    Mironov, A.A.2    Rakhmaninova, A.B.3
  • 6
    • 0026686241 scopus 로고
    • Analysis of protein sheet topologies by graph theoretical methods
    • Koch I, Kaden F, Selbig J. Analysis of protein sheet topologies by graph theoretical methods. Proteins 1992;12:314-323.
    • (1992) Proteins , vol.12 , pp. 314-323
    • Koch, I.1    Kaden, F.2    Selbig, J.3
  • 7
    • 0030629298 scopus 로고    scopus 로고
    • Detection of distant structural similarities in a set of proteins using a fast graph-based method
    • Koch I, Lengauer T. Detection of distant structural similarities in a set of proteins using a fast graph-based method. Proc Int Conf Intell Syst Mol Biol 1997;5:167-178.
    • (1997) Proc Int Conf Intell Syst Mol Biol , vol.5 , pp. 167-178
    • Koch, I.1    Lengauer, T.2
  • 8
    • 0030016158 scopus 로고    scopus 로고
    • An algorithm for finding maximal common subtopologies in a set of protein structures
    • Koch I, Lengauer T, Wanke E. An algorithm for finding maximal common subtopologies in a set of protein structures. J Comput Biol 1996;3:289-306. (Pubitemid 26243846)
    • (1996) Journal of Computational Biology , vol.3 , Issue.2 , pp. 289-306
    • Koch, I.1
  • 16
    • 3142538754 scopus 로고    scopus 로고
    • Seeing GroEL at 6 A resolution by single particle electron cryomicroscopy
    • DOI 10.1016/j.str.2004.05.006, PII S0969212604001698
    • Ludtke SJ, Chen DH, Song JL, Chuang DT, Chiu W. Seeing GroEL at 6 A resolution by single particle electron cryomicroscopy. Structure 2004;12:1129-1136. (Pubitemid 38900755)
    • (2004) Structure , vol.12 , Issue.7 , pp. 1129-1136
    • Ludtke, S.J.1    Chen, D.-H.2    Song, J.-L.3    Chuang, D.T.4    Chiu, W.5
  • 17
    • 0035906702 scopus 로고    scopus 로고
    • Bridging the information gap: Computational tools for intermediate resolution structure interpretation
    • DOI 10.1006/jmbi.2001.4633
    • Jiang W, Baker ML, Ludtke SJ, Chiu W. Bridging the information gap: computational tools for intermediate resolution structure interpretation. J Mol Biol 2001;308:1033-1044. (Pubitemid 32574375)
    • (2001) Journal of Molecular Biology , vol.308 , Issue.5 , pp. 1033-1044
    • Jiang, W.1    Baker, M.L.2    Ludtke, S.J.3    Chiu, W.4
  • 18
    • 20444490870 scopus 로고    scopus 로고
    • Determining protein topology from skeletons of secondary structures
    • DOI 10.1016/j.jmb.2005.04.064, PII S0022283605004973
    • Wu Y, Chen M, Lu M, Wang Q, Ma J. Determining protein topology from skeletons of secondary structures. J Mol Biol 2005;350:571-586. (Pubitemid 40828915)
    • (2005) Journal of Molecular Biology , vol.350 , Issue.3 , pp. 571-586
    • Wu, Y.1    Chen, M.2    Lu, M.3    Wang, Q.4    Ma, J.5
  • 19
    • 0041507094 scopus 로고    scopus 로고
    • A structural-informatics approach for mining beta-sheets: Locating sheets in intermediate-resolution density maps
    • DOI 10.1016/S0022-2836(03)00859-3
    • Kong Y, Ma J. A structural-informatics approach for mining beta-sheets: locating sheets in intermediate-resolution density maps. J Mol Biol 2003;332:399-413. (Pubitemid 37013508)
    • (2003) Journal of Molecular Biology , vol.332 , Issue.2 , pp. 399-413
    • Kong, Y.1    Ma, J.2
  • 20
    • 2342538953 scopus 로고    scopus 로고
    • alpha traces for beta-strands in intermediate-resolution density maps
    • DOI 10.1016/j.jmb.2004.03.038, PII S0022283604003146
    • Kong Y, Zhang X, Baker TS, Ma J. A Structural-informatics approach for tracing beta-sheets: building pseudo-C (alpha) traces for beta-strands in intermediate-resolution density maps. J Mol Biol 2004;339:117-130. (Pubitemid 38569693)
    • (2004) Journal of Molecular Biology , vol.339 , Issue.1 , pp. 117-130
    • Kong, Y.1    Zhang, X.2    Baker, T.S.3    Ma, J.4
  • 22
    • 33846061281 scopus 로고    scopus 로고
    • Identification of Secondary Structure Elements in Intermediate-Resolution Density Maps
    • DOI 10.1016/j.str.2006.11.008, PII S0969212606004722
    • Baker ML, Ju T, Chiu W. Identification of secondary structure elements in intermediate-resolution density maps. Structure 2007;15:7-19. (Pubitemid 46073771)
    • (2007) Structure , vol.15 , Issue.1 , pp. 7-19
    • Baker, M.L.1    Ju, T.2    Chiu, W.3
  • 23
    • 0033377664 scopus 로고    scopus 로고
    • EMAN: Semi-automated software for high resolution single particle reconstructions
    • Ludtke SJ, Baldwin PR, Chiu W. EMAN: Semi-automated software for high resolution single particle reconstructions. J Struct Biol 1999;128:82-97.
    • (1999) J Struct Biol , vol.128 , pp. 82-97
    • Ludtke, S.J.1    Baldwin, P.R.2    Chiu, W.3
  • 24
    • 38949092920 scopus 로고    scopus 로고
    • Protein Structure Fitting and Refinement Guided by Cryo-EM Density
    • DOI 10.1016/j.str.2007.11.016, PII S0969212608000130
    • Topf M, Lasker K, Webb B, Wolfson H, Chiu W, Sali A. Protein structure fitting and refinement guided by cryo-EM density. Structure 2008;16:295-307. (Pubitemid 351215215)
    • (2008) Structure , vol.16 , Issue.2 , pp. 295-307
    • Topf, M.1    Lasker, K.2    Webb, B.3    Wolfson, H.4    Chiu, W.5    Sali, A.6
  • 25
    • 33645075435 scopus 로고    scopus 로고
    • Refinement of protein structures by iterative comparative modeling and CryoEM density fitting
    • Topf M, Baker ML, Marti-Renom MA, Chiu W, Sali A. Refinement of protein structures by iterative comparative modeling and CryoEM density fitting. J Mol Biol 2006;357:1655-1668.
    • (2006) J Mol Biol , vol.357 , pp. 1655-1668
    • Topf, M.1    Baker, M.L.2    Marti-Renom, M.A.3    Chiu, W.4    Sali, A.5
  • 26
    • 44049103480 scopus 로고    scopus 로고
    • Deriving topology and sequence alignment for the helix skeleton in low-resolution protein density maps
    • DOI 10.1142/S0219720008003357, PII S0219720008003357
    • Lu Y, He J, Strauss CE. Deriving topology and sequence alignment for the helix skeleton in low-resolution protein density maps. J Bioinform Comput Biol 2008;6:183-201. (Pubitemid 351711906)
    • (2008) Journal of Bioinformatics and Computational Biology , vol.6 , Issue.1 , pp. 183-201
    • Lu, Y.1    He, J.2    Strauss, C.E.M.3
  • 27
    • 33750479009 scopus 로고    scopus 로고
    • Ab initio modeling of the herpesvirus VP26 core domain assessed by cryoEM density
    • DOI 10.1371/journal.pcbi.0020146
    • Baker ML, Jiang W, Wedemeyer WJ, Rixon FJ, Baker D, Chiu W. Ab initio modeling of the herpesvirus VP26 core domain assessed by CryoEM density. PLoS Comput Biol 2006;2:e146. (Pubitemid 44656524)
    • (2006) PLoS Computational Biology , vol.2 , Issue.10 , pp. 1313-1324
    • Baker, M.L.1    Jiang, W.2    Wedemeyer, W.J.3    Rixon, F.J.4    Baker, D.5    Chiu, W.6
  • 29
    • 33750402176 scopus 로고    scopus 로고
    • A new representation for protein secondary structure prediction based on frequent patterns
    • DOI 10.1093/bioinformatics/btl453
    • Birzele F, Kramer S. A new representation for protein secondary structure prediction based on frequent patterns. Bioinformatics 2006;22:2628-2634. (Pubitemid 44642601)
    • (2006) Bioinformatics , vol.22 , Issue.21 , pp. 2628-2634
    • Birzele, F.1    Kramer, S.2
  • 30
    • 0034044314 scopus 로고    scopus 로고
    • The PSIPRED protein structure prediction server
    • McGuffin LJ, Bryson K, Jones DT. The PSIPRED protein structure prediction server. Bioinformatics 2000;16:404-405. (Pubitemid 30417087)
    • (2000) Bioinformatics , vol.16 , Issue.4 , pp. 404-405
    • McGuffin, L.J.1    Bryson, K.2    Jones, D.T.3
  • 31
    • 0036568279 scopus 로고    scopus 로고
    • Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles
    • DOI 10.1002/prot.10082
    • Pollastri G, Przybylski D, Rost B, Baldi P. Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles. Proteins 2002;47:228-235. (Pubitemid 34263335)
    • (2002) Proteins: Structure, Function and Genetics , vol.47 , Issue.2 , pp. 228-235
    • Pollastri, G.1    Przybylski, D.2    Rost, B.3    Baldi, P.4
  • 33
    • 0031566950 scopus 로고    scopus 로고
    • Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation
    • DOI 10.1006/jmbi.1996.0758
    • Bahar I, Jernigan RL. Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation. J Mol Biol 1997;266:195-214. (Pubitemid 27170528)
    • (1997) Journal of Molecular Biology , vol.266 , Issue.1 , pp. 195-214
    • Bahar, I.1    Jernigan, R.L.2
  • 34
    • 0026785519 scopus 로고
    • Contact potential that recognizes the correct folding of globular proteins
    • Maiorov VN, Crippen GM. Contact potential that recognizes the correct folding of globular proteins. J Mol Biol 1992;227:876-888.
    • (1992) J Mol Biol , vol.227 , pp. 876-888
    • Maiorov, V.N.1    Crippen, G.M.2
  • 35
    • 33845377127 scopus 로고
    • Estimation of effective interresidue contact energies from protein crystal structures: Quasi-chemical approximation
    • Miyazawa S, Jernigan RL. Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation. Macromolecules 1985;18:534-552.
    • (1985) Macromolecules , vol.18 , pp. 534-552
    • Miyazawa, S.1    Jernigan, R.L.2
  • 36
    • 0029919190 scopus 로고    scopus 로고
    • Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading
    • DOI 10.1006/jmbi.1996.0114
    • Miyazawa S. Jernigan RL. Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading. J Mol Biol 1996;256:623-644. (Pubitemid 26107211)
    • (1996) Journal of Molecular Biology , vol.256 , Issue.3 , pp. 623-644
    • Miyazawa, S.1    Jernigan, R.L.2
  • 38
    • 0017021957 scopus 로고
    • Medium- And long-range interaction parameters between amino acids for predicting three-dimensional structures of proteins
    • Tanaka S, Scheraga HA. Medium- and long-range interaction parameters between amino acids for predicting three-dimensional structures of proteins. Macromolecules 1976;9:945-950.
    • (1976) Macromolecules , vol.9 , pp. 945-950
    • Tanaka, S.1    Scheraga, H.A.2
  • 39
    • 0025341310 scopus 로고
    • Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins
    • Sippl MJ. Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins. J Mol Biol 1990;213:859-883.
    • (1990) J Mol Biol , vol.213 , pp. 859-883
    • Sippl, M.J.1
  • 40
    • 0029987862 scopus 로고    scopus 로고
    • Energy functions that discriminate X-ray and near-native folds from well-constructed decoys
    • DOI 10.1006/jmbi.1996.0256
    • Park B, Levitt M. Energy functions that discriminate X-ray and near native folds from well-constructed decoys. J Mol Biol 1996;258:367-392. (Pubitemid 26131738)
    • (1996) Journal of Molecular Biology , vol.258 , Issue.2 , pp. 367-392
    • Park, B.1    Levitt, M.2
  • 41
    • 0028897718 scopus 로고
    • Computer modeling of protein folding: Conformational and energetic analysis of reduced and detailed protein models
    • Monge A, Lathrop EJ, Gunn J R, Shenkin PS, Friesner RA. Computer modeling of protein folding: conformational and energetic analysis of reduced and detailed protein models. J Mol Biol 1995;247:995-1012.
    • (1995) J Mol Biol , vol.247 , pp. 995-1012
    • Monge, A.1    Lathrop, E.J.2    Gunn, J.R.3    Shenkin, P.S.4    Friesner, R.A.5
  • 42
    • 0017157584 scopus 로고
    • A simplified representation of protein conformations for rapid simulation of protein folding
    • Levitt M. A simplified representation of protein conformations for rapid simulation of protein folding. J Mol Biol 1976;104:59-107.
    • (1976) J Mol Biol , vol.104 , pp. 59-107
    • Levitt, M.1
  • 43
    • 0025319917 scopus 로고
    • Conformations of folded proteins in restricted spaces
    • Covell DG, Jernigan RL. Conformations of folded proteins in restricted spaces. Biochemistry 1990;29:3287-3294.
    • (1990) Biochemistry , vol.29 , pp. 3287-3294
    • Covell, D.G.1    Jernigan, R.L.2
  • 44
    • 0003408570 scopus 로고
    • Oxford: IRL Press, Vol 1: ISBN: 0199633614; Vol 2: ISBN: 0199633622
    • Singh J, Thornton J. Atlas of protein side-chain interactions, Vols. I & II. Oxford: IRL Press, Vol 1: ISBN: 0199633614; Vol 2: ISBN: 0199633622; 1992.
    • (1992) Atlas of Protein Side-chain Interactions , vol.1-2
    • Singh, J.1    Thornton, J.2
  • 45
    • 27844568915 scopus 로고    scopus 로고
    • Automatic program for peak detection and deconvolution of multi-overlapped chromatographic signals: Part II: Peak model and deconvolution algorithms
    • DOI 10.1016/j.chroma.2005.03.072, PII S0021967305006394, Chemical Separations and Chemometrics
    • Vivo-Truyols G, Torres-Lapasio JR, van Nederkassel AM, Vander Heyden Y, Massart DL. Automatic program for peak detection and deconvolution of multi-overlapped chromatographic signals part II: peak model and deconvolution algorithms. J Chromatogr A 2005;1096:146-155. (Pubitemid 41653133)
    • (2005) Journal of Chromatography a , vol.1096 , Issue.1-2 , pp. 146-155
    • Vivo-Truyols, G.1    Torres-Lapasio, J.R.2    Van Nederkassel, A.M.3    Vander Heyden, Y.4    Massart, D.L.5
  • 47
    • 0025633179 scopus 로고
    • A fully automated chromatographic peak detection and treatment software for multi-user multi-task computers
    • Cardot PJ, Trolliard P, Tembely S. A fully automated chromatographic peak detection and treatment software for multi-user multi-task computers. J Pharm Biomed Anal 1990;8:755-759.
    • (1990) J Pharm Biomed Anal , vol.8 , pp. 755-759
    • Cardot, P.J.1    Trolliard, P.2    Tembely, S.3
  • 48
    • 28444450919 scopus 로고    scopus 로고
    • Multicomponent peak modeling of protein secondary structures: Comparison of gaussian with lorentzian analytical methods for plant feed and seed molecular biology and chemistry research
    • Yu P. Multicomponent peak modeling of protein secondary structures: comparison of gaussian with lorentzian analytical methods for plant feed and seed molecular biology and chemistry research. Appl Spectrosc 2005;59:1372-1380.
    • (2005) Appl Spectrosc , vol.59 , pp. 1372-1380
    • Yu, P.1
  • 50
    • 17444397116 scopus 로고    scopus 로고
    • Porter: A new, accurate server for protein secondary structure prediction
    • DOI 10.1093/bioinformatics/bti203
    • Pollastri G, McLysaght A. Porter: a new, accurate server for protein secondary structure prediction. Bioinformatics 2005;21:1719-1720. (Pubitemid 40542742)
    • (2005) Bioinformatics , vol.21 , Issue.8 , pp. 1719-1720
    • Pollastri, G.1    McLysaght, A.2
  • 52
    • 0021819411 scopus 로고
    • THERMODYNAMICAL APPROACH to the TRAVELING SALESMAN PROBLEM: AN EFFICIENT SIMULATION ALGORITHM
    • Cerny V. A thermodynamical approach to the travelling salesman problem: an efficient simulation algorithm. J Optimization Theory Appl 1985;45:41-51. (Pubitemid 15462741)
    • (1985) Journal of Optimization Theory and Applications , vol.45 , Issue.1 , pp. 41-51
    • Cerny, V.1
  • 53
    • 0017411710 scopus 로고
    • The protein data bank: A computer based archival file for macromolecular structures
    • Bernstein FC, Koetzle TF, Williams GJ, Meyer EF, Jr, Brice MD, Rodgers JR, Kennard O, Shimanouchi T, Tasumi M. The Protein Data Bank: a computer-based archival file for macromolecular structures. J Mol Biol 1977;112:535-542. (Pubitemid 8109216)
    • (1977) Journal of Molecular Biology , vol.112 , Issue.3 , pp. 535-542
    • Bernstein, F.C.1    Koetzle, T.F.2    Williams, G.J.B.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.